[Chimera-users] Drawing H-bond

[Elaine Meng]

On Apr 9, 2008, at 11:59 AM, Ibrahim Moustafa wrote:
>
>    Recently I’m switching from my favorite molecular graphics  
> software “Pymol” to Chimera.
> I find chimera very useful in terms of structural analysis and easy  
> to drive through the smooth command line.
> I have a question regarding drawing H-bond in figures for  
> publications: Is there a way to instruct the program to draw a H-bond
> Between two particular atoms in dotted (dashed) line style?
>
>   I know that ‘hbond’ does a decent job in finding the H-bonds  
> represented by solid lines. However, in the cases I tried the H- 
> bond network found by ‘hbond’
> Is a bit complicated and simplification is necessary for the  
> figure. I wonder if the user can have a control over which  
> “psudobond” to draw between what atoms.
> This would make the program very handy for me.

Hi Ibrahim,
Thanks for your kind words!

I just wanted to give an example of using PseudoBond Reader.  A few  
years ago I used it to make a paper figure that shows crosslinks  
engineered into rhodopsin.  I won't go into the details of all the  
colors, but black lines represent disulfide crosslinks that inhibit  
activation and gold (actually "goldenrod") lines shows disulfides  
that do not inhibit activation.

The structure is 1f88, and to show just chain A in the figure, I used  
commands like:

open 1f88
del ~ :.a
chain @ca
focus
ribbon
ribrepr smooth
set bg_color white
color cyan

Then I started PseudoBond Reader (under Tools... Depiction) and used  
it to open a text file listing the atom pairs and the desired  
pseudobond colors.  In the file-opening dialog you can also specify  
the line width (unfortunately not whether the lines are dashed,  
however) and pseudobond group name.  Contents of the text file are  
simply:

:65 at ca :316 at ca goldenrod
:110 at ca :187 at ca goldenrod
:136 at ca :222 at ca black
:136 at ca :225 at ca goldenrod
:139 at ca :225 at ca goldenrod
:140 at ca :222 at ca black
:140 at ca :225 at ca goldenrod
:138 at ca :251 at ca forest green
:139 at ca :247 at ca black
:139 at ca :248 at ca black
:139 at ca :249 at ca black
:139 at ca :250 at ca black
:139 at ca :251 at ca black
:140 at ca :316 at ca yellow
:198 at ca :276 at ca goldenrod
:200 at ca :276 at ca goldenrod
:204 at ca :276 at ca goldenrod
:246 at ca :312 at ca black
:242 at ca :338 at ca goldenrod
:245 at ca :338 at ca goldenrod

Although not included in this example, you can also specify labels on  
the individual pseudobonds in the text file.  You would still have to  
use PseudoBond Panel, choose the group, and set its attributes to  
make the lines dashed, however.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html